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The story takes place in feudal Japan and follows the adventures of Jubei Kibagami, a mercenary ninja who is given a duty to guard the Dragon Stone and to protect the Priestess of Light (Shigure) from the Hiruko Clan and the Kimon Shu. He is aided by the government spy Dakuan and the thief Tsubute.

Jubei Kibagami (牙神 獣兵衛,Kibagami Jūbē) is the protagonist of the show. He is a wandering vagabond ninja who wants nothing to do but rest until one day, he got himself involved in a battle between the Hiruko and the Kimon Clan. Later, one of the Hiruko Clan members gave him a Dragon Stone in which he must give it to the light maiden, Shigure. Now he is on an adventure to give the Dragon Stone to Shigure and to protect her from both the Hiruko and the Kimon Clan.

All her life, Shigure (しぐれ,Shigure) has lived in the mountains until her village was burnt to the ground by the Kimon Clan. Lost and confused, she doesn't know what to do until she meets up with Dakuan and Tsubute and realizes that she must go to the village of Yagyu. Shigure is known as the Light Maiden and is highly treasured by her fellow people.

Tsubute (つぶて,Tsubute) is a very sneaky mountain thief who ends up tagging along with Dakuan and Shigure and he always tries to steal the Dragon Stone whenever he can. He often acts tough but is almost always turnerd down and actually isn't very tough.

Rouga is a stern shinobi that wears an iron mask. He is the one responsible for stealing the Dragon Stone from the Hiruko to give to the light maiden. He fails in his quest but is able to give the stone to Jubei for safekeeping. He has werewolf-like abilities, his full transformation occurring when he removes his mask. He is killed during the Kimon clan's assault on Shigure's village by Ubume's rodents.

Mozuku is a goblin-like shinobi with green skin and a specialized gland on his forehead that spews a thick spiderweb substance. He was sent after Roga to retrieve the Dragon Stone but attacked by the Kimon ninja instead. He was killed by Ubume's rodents.

Nekome is a maliciously playful kunoichi with feline-like feet and claws. She attacks Jubei in an attempt to recapture the Dragon Stone, unaware that Roga entrusted it to him. She is defeated in battle by Jubei.

Nubatama is a coquettish kunoichi with long dark hair that she can manipulate freely to attack her enemies. She first tries to seduce Jyashi who spurns her advances and is then run through from behind by Rengoku. She survives, however, only to return and be slain in battle by Rengoku.

Azami is a surreptitious kunoichi who can extend her limbs into root-like appendages which she can use as weapons as well as merge with the surrounding flora to manipulate their root systems. She works covertly from a safe distance using the roots to attack her opponents. She manages to steal the Dragon Stone from Jubei but splits it into two halves in the process. She retains one half but loses it later to Kitsunebi. She is attacked and wounded by Kawahori and dies, but not before giving Jubei half of the Dragon Stone.

Dakatsu is a grotesque shinobi with a oddly-shaped body and a tail with a sting capable to kill a bear in seconds. He tries to manipulate Rengoku by helping her to kill Jubei in exchange for the stone and her own limbs, which he believes they will make him less ugly, but he is fooled and murdered at the end by Rengoku when she controls her body parts on him and forces him to drown in a river.

Hakurou is a venomous shinobi with a body covered in reptile scales and a lizard-like face. His skin is thick enough to withstand an attack from Jubei. His back is covered with spines that he can rapid fire at his opponent. Jubei kills him by ramming his sword down his throat.

Nenmu is a bodiless shinobi that exists as only a single eye and a purple ooze-like substance. He gains possession of a host by forcefully invading his victim's body and taking control, living on even after they die. He takes possession of a number of travelers taking refuge from the rain along with Jubei. One of the travelers, a mother traveling with her son, is possessed but gains some control and walks into a fire killing Nenmu.

Zoufu is a self-possessed Japanese man with a Western swordfighting style. He has a monstrous parasite that has lived in his abdomen most, if not all, of his life. He has tried numerous times to kill the beast by coaxing it out by putting his life in danger, as the creature always comes to his aid during battle to preserve its host. His duel with Jubei leads to him finally killing the beast only to realize that its death meant his own as well.

Rokai is an exuberant shinobi with a voracious appetite and an effeminate disposition. He was imprisoned by his own clan, perhaps for being so annoying, but escaped to find Shigure, the light maiden. He has the ability to expand his squat frame into a massively obese grub-like form. He is killed by Yamidoro while trying to protect Jubei.

An unnamed little girl with the ability to turn into an monstrous-looking hag by growing a second face in the back of her head. She is very agile and fights with a long cloth with sharp edges. After trying to steal the stone in a ship, she is defeated and befriended by Jubei, but is accidentally killed by Renya after she tries to stop him from fighting Kibagami.

Mokuji is an infant sized shinobi that lives stuffed in the mouth of Ashizo, a big, green dumb shinobi. Mokuji seems to be the brains whereas Ashizo is the brawn. Ashizo is run through by ninja under the spell of Utsushiei, then decapitated. Mokuji is left defenseless and is stabbed by Utsushiei disguised as Shigure.

Anden Yamidoro is the leader of the Kimon Clan who wants to overthrow the Hiruko Clan. He wants the Dragon Stone so he can use its fortune to overtake the shogun. He is later revealed to be the brother of Mufu, leader of the Hiruko clan. Yamidoro and Mufu are identical twins who reside in what is later revealed to be robotic bodies.

Magai is a diminutive, meakeup-wearing shinobi that wields a giant spear; attached is a peddle-powered umbrella that spins and flies like a helicopter. While trying to steal the Dragon Stone from Rouga, he is cut down by Jubei.

Ubume is a malevolent kunoichi with a body of semi-metamorphing flesh. Her son, Yadorigi (voiced by Akio Suyama) is melded with her body and can come to the surface to form his own tiny body. Also melded with her body is a small army of razor-sharp toothed rodents that can freely attack her opponent as well as merge into one giant rodent. She carries a flaming thorn whip. She attempts to steal the Dragon Stone from Roga, but is scared off by Jubei's intervention. She later returns to attack Shigure's village, only to be slain by Jubei, which also causes the deaths of Yadorigi and her rodents.

Jyashi is a serene shinobi who carries a katana and has a specialized eye socket that houses a hypnosis device that transports his opponents to an illusory world. He can also take an eye from a corpse and place it within his eye socket to see its final images. His left arm is mechanical and has an automatic launcher that fires arrows at a tremendous rate. He is the brother of Rengoku.

Rengoku is a mysterious kunoichi with a unique body and talent for self-surgery. Rengoku can sew replacement or extra body parts to herself. She has four arms and a variety of stitch patterns across her body. Her arms stretch out to resemble spindly spider legs and she is viewed as a monster by local villagers. She is obsessed with her brother to the point of incest. His death sent her on a path of vengeance toward Jubei, instead of focusing on collecting the Dragon Stone. She is killed by Yamidoro, while in her madness mistaking him for Jyashi.

Kitsunebi is a blood thirsty shinobi that possesses a semi-transparent glass-like body, through which a blue flame can be seen in his chest. He is capable of controlling a swarm of moths that sprinkle a sleeping powder on his enemies. With concentration and mysticism he calls forth a giant moth composed of red energy. Like many of the ninja, he has a wicked personality, exhibited in his attempted rape of Azami. He is killed by Jubei in a sulfur pit in which his moths were repelled.

Tobizaru is a shinobi with a baboon-like appearance. He commands a horde of lesser monkey ninja. He uses strange angled swords as well as retractable wrist mounted straight swords. He is actually much smaller than he first appears, as he wears an anthropomorphic mechanical suit which just shows his head. He is killed by an explosion caused by Yamidoro in an attempt to kill Jubei.

Gouten appears to be an inhumanly massive shinobi that wears tank-like armor and carries two giant clubs that act as wheels on which he rolls like a car. On his back are four mounted flamethrowers. All this is a façade, though, as Gouten is actually a normal sized ninja that drives the enormous body like a tank. He also controls a little mechanical girl that acts as a spy, and a mechanical bird that acts as a messenger. He is killed by a trick of Dakuan's that resulted in him falling to the bottom of a lake where he drowned, unable to escape in time.

Aizen is a manipulative shinobi who has a golden rifle in place of his right arm. He tries to convince Tatsunosuke into joining the Kimon clan. He is killed when Jubei flings his sword into Aizen's forehead.

Kawahori is a snide shinobi that has gray skin and white hair, complete with pointed ears and fangs. He has a pair of mechanical bat wings granting him flight, and he controls a colony of bats that he uses to enshroud his opponent. He can also extend his tongue as a proboscis. He is killed by Jubei while attempting to steal the second half of the Dragon Stone from Azami. His name means bat.

Utsushiei is a conniving kunoichi with a shape shifting ability. She has special acupuncture pins she places into the necks of others that allows her to control their minds. She also has the ability to take the form of others by manipulating her own flesh (she manifests as Shigure, after controlling/seducing the Light Maiden, and manages to fool her companions flawlessly). She is killed by Yamidoro in his attempt to send Jubei into a volcano.

Tatsunosuke, calling himself Mr. Diamond, is a thief with the ability to generate diamond blades from his body. He later meets up with Tsubute and they become friends. He is totally useless when he is hungry.

A ninja named Roga from the Hiruko Clan steals the Dragon Stone from the Hiruko Clan, and a huge clan fight over the stone ensues. Ninja hero Jubei interrupts the fight to take the jewel and, after Roga asks him, accepts the task of delivering it to Shigure - the Priestess of Light. Roga dies sacrificing himself for the Light Maiden, living in the light for once before he dies.

2

"Departure""Tabidachi" (旅立ち)

22 April 2003 (2003-04-22)

Jubei must find a way to give the Dragon Stone to Shigure whilst being hunted down by both the Hiruko Clan and the Kimon Shu. After her village is destroyed, Shigure wanders helplessly until she meets Tsubute and Dakuan who are willing to help her find out who she really is.

3

"Forbidden Love" (邪恋慟哭)

29 April 2003 (2003-04-29)

Two members of the Kimon Shu, Jyashi and Rengoku, fight Jubei and Dakuan for the Dragon Stone and the Priestess of Light. Jyashi is killed by Jubei, and Rengoku, broken, swears to avenge his death.

4

"Broken Stone" (割れた宝玉)

6 May 2003 (2003-05-06)

Jubei is ambushed by strange roots sent by a Hiruko Ninja, and during the struggle for the stone it is split in two, and the roots take one half. Later a Kimon Shu ninja steals the Hiruko Ninja's half, and sends it back to the Kimon Shu base. Jubei tries to get the stone back, only to find that it is too late.

5

"Diamond Child" (金剛童子)

13 May 2003 (2003-05-13)

After stealing the Dragon Stone from Shigure, Tsubute meets Tatsunosuke, a failed yet talented thief who also wants to steal the Dragon Stone. A Kimon Shu member named Aizen wants Tatsunosuke to join him.

6

"Shelter from the Rain" (雨宿り)

20 May 2003 (2003-05-20)

As the rain pours down, Jubei is attacked and poisoned. Seeking shelter from the rain, he meets up with a boy and his mother who cure him of the poison. But the creature that poisoned Jubei isn't dead and when killed can leave its host to take another.

7

"Blossom" (蕾)

27 May 2003 (2003-05-27)

Still after the stone, the root-woman from episode 4 manages to steal Jubei's half of it, but along the way, a Kimon Shu member attacks her. With the help of Jubei, she survives to tell him of the Hiruko, and return the stone.

8

"The Fate of Rengoku" (煉獄昇天)

3 June 2003 (2003-06-03)

After her brother's death, Rengoku is willing to do whatever it takes to kill Jubei even if it means losing her mind, and several limbs.

9

"A Dragon Within" (はらわたに龍)

17 June 2003 (2003-06-17)

A man named Zofu saves Shigure from the Yagyu clan. He reveals the secrets of the Hiruko Clan to her. He also wishes to get rid of an old friend that he carries. With Jubei's help, he might get a chance.

10

"The Heart of the Hiruko" (ヒルコの真心)

24 June 2003 (2003-06-24)

Shigure has an unexpected friend by her side, Rokai - a Hiruko Ninja. He fails to protect her as the Kimon Shu have sent out their elite to finish the job. Shigure is finally captured.

11

"Yagyu Renya""Yagyū Ren'ya" (柳生連夜)

1 July 2003 (2003-07-01)

Jubei must save Shigure by taking a ship to another part of Japan. Along the way, he meets Yagyu Renya, a cold-blooded samurai who has the same goals as Jubei, to find the Dragon Stone and Shigure. Not only that, there seems to be a killer on the ship and everyone is in danger.

12

"Dynasty Restoration""Ōchō Fukkoku" (王朝復活)

8 July 2003 (2003-07-08)

Jubei saves Shigure from the Kimon Shu with the help of the Hiruko. But as they get closer to the ancient Hiruko Lands, it becomes evident that all is not what it seems, and the Kimon Shu have the upper hand once again.

13

"Farewell Jubei" (青天飄飄)

15 July 2003 (2003-07-15)

Now Shigure's destiny is unveiled and she must walk the path of the Priestess of Light. Will she be able to face her destiny without Jubei by her side?

Ninja Scroll is an original soundtrack to Japanese TV series of the same name, written and directed by Yoshiaki Kawajiri. Taking place in ancient Japan, Ninja Scroll is the story of a wandering Ninja warrior named Jubei.[1] The music for the soundtrack is co-scored by Kitaro and Peter (Peas) McEvilley.[2]